1
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Zhao Z, Yan W, Weng X. RNA modifications identification based on chemical reactions. Bioorg Med Chem 2024; 111:117861. [PMID: 39079454 DOI: 10.1016/j.bmc.2024.117861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/24/2024] [Accepted: 07/25/2024] [Indexed: 08/24/2024]
Abstract
RNA modification identification is an emerging field in epigenetics due to its indispensable regulatory role in the cell life cycle. With advancements in identification methods, an increasing number of RNA modifications has been discovered, thereby driving the development of more efficient and accurate techniques for localizing modified RNAs and elucidating their functions. High-throughput sequencing approaches for modified RNA detection can be categorized into antibody-based, enzymatic-based, and chemical-labeling-based methods. Given the intrinsic chemical reactions involved in all biochemical processes, we provide a comprehensive review of recent advancements in artificial chemical labeling and transformations of ten distinct RNA modifications and their applications in sequencing. Our aim is to contribute to a deeper understanding of the mechanisms underlying these modifications. We focus on the chemical reactions associated with RNA modifications and briefly compare the advantages and disadvantages of detection methods based on these reactions. Additionally, we introduce several approaches that identify multiple modifications through chemical labeling. As the field of RNA modification research continues to expand, we anticipate that the techniques and insights presented in this review will serve as a valuable resource for future studies aimed at further elucidating the functional roles of RNA modifications in biological processes.
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Affiliation(s)
- Zhengjia Zhao
- Department of Clinical Laboratory, Center for Gene Diagnosis, and Program of Clinical Laboratory Medicine, Zhongnan Hospital of Wuhan University, China; College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan 430072, China
| | - Weikai Yan
- Department of Clinical Laboratory, Center for Gene Diagnosis, and Program of Clinical Laboratory Medicine, Zhongnan Hospital of Wuhan University, China; College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan 430072, China
| | - Xiaocheng Weng
- Department of Clinical Laboratory, Center for Gene Diagnosis, and Program of Clinical Laboratory Medicine, Zhongnan Hospital of Wuhan University, China; College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan 430072, China.
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2
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Mothersole R, Wynne FT, Rota G, Mothersole MK, Liu J, Van Hamme JD. Formation of CoA Adducts of Short-Chain Fluorinated Carboxylates Catalyzed by Acyl-CoA Synthetase from Gordonia sp. Strain NB4-1Y. ACS OMEGA 2023; 8:39437-39446. [PMID: 37901528 PMCID: PMC10601079 DOI: 10.1021/acsomega.3c05147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 09/20/2023] [Indexed: 10/31/2023]
Abstract
Perfluoroalkyl and polyfluoroalkyl substances (PFAS) make up a group of anthropogenic chemicals with a myriad of applications. However, some PFAS have been shown to negatively impact human health and the environment, leading to increased regulation, with some countries making efforts to phase out their use. PFAS fate in the environment is driven by physical, chemical, and biological processes, with microbial communities in matrices such as soil and sewage sludge being known to generate a range of low-molecular-weight PFAS metabolites. Proposed metabolic intermediates for both mixed and pure microbial cultures include fluorinated carboxylates that may be activated by CoA prior to β-oxidation and defluorination, although thus far, no PFAS-CoA adducts have been reported. Herein, we expressed and purified acyl-CoA synthetase (ACS) from the soil bacterium Gordonia sp. strain NB4-1Y and performed an analysis of substrate scope and enzyme kinetics using fluorinated and nonfluorinated carboxylates. We determined that ACS was able to catalyze the formation of CoA adducts of 3,3,3-trifluoropropionic acid, 5,5,5-trifluoropentanoic acid, 4,5,5-trifluoropent-4-enoic acid, and 4,4,5,5,5-pentafluoropentanoic acid. Kinetic analysis revealed a 90-98% decrease in kcat between nonfluorinated carboxylates and their fluorinated analogues. This provides evidence to validate proposed enzymatic pathways for microbial PFAS metabolism that proceed via an activation step involving the formation of CoA adducts.
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Affiliation(s)
- Robert
G. Mothersole
- Department
of Biological Sciences, Thompson Rivers
University, 805 TRU Way, Kamloops, BC V2C 0C8, Canada
| | - Foster T. Wynne
- Department
of Biological Sciences, Thompson Rivers
University, 805 TRU Way, Kamloops, BC V2C 0C8, Canada
| | - Gaia Rota
- Department
of Biological Sciences, Thompson Rivers
University, 805 TRU Way, Kamloops, BC V2C 0C8, Canada
| | - Mina K. Mothersole
- Department
of Biological Sciences, Thompson Rivers
University, 805 TRU Way, Kamloops, BC V2C 0C8, Canada
| | - Jinxia Liu
- Department
of Civil Engineering, McGill University, 817 Sherbrooke Street West, Montreal, QC H3A
0C3, Canada
| | - Jonathan D. Van Hamme
- Department
of Biological Sciences, Thompson Rivers
University, 805 TRU Way, Kamloops, BC V2C 0C8, Canada
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3
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Yan S, Lu Z, Yang W, Xu J, Wang Y, Xiong W, Zhu R, Ren L, Chen Z, Wei Q, Liu SM, Feng T, Yuan B, Weng X, Du Y, Zhou X. Antibody-Free Fluorine-Assisted Metabolic Sequencing of RNA N4-Acetylcytidine. J Am Chem Soc 2023; 145:22232-22242. [PMID: 37772932 DOI: 10.1021/jacs.3c08483] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
N4-Acetylcytidine (ac4C) has been found to affect a variety of cellular and biological processes. For a mechanistic understanding of the roles of ac4C in biology and disease, we present an antibody-free, fluorine-assisted metabolic sequencing method to detect RNA ac4C, called "FAM-seq". We successfully applied FAM-seq to profile ac4C landscapes in human 293T, HeLa, and MDA cell lines in parallel with the reported acRIP-seq method. By comparison with the classic ac4C antibody sequencing method, we found that FAM-seq is a convenient and reliable method for transcriptome-wide mapping of ac4C. Because this method holds promise for detecting nascent RNA ac4C modifications, we further investigated the role of ac4C in regulating chemotherapy drug resistance in chronic myeloid leukemia. The results indicated that drug development or combination therapy could be enhanced by appreciating the key role of ac4C modification in cancer therapy.
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Affiliation(s)
- Shen Yan
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, Hubei, PR China
| | - Ziang Lu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, Hubei, PR China
| | - Wei Yang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, Hubei, PR China
| | - Jinglei Xu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, Hubei, PR China
| | - Yafen Wang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, Hubei, PR China
| | - Wei Xiong
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, Hubei, PR China
| | - Rongjie Zhu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, Hubei, PR China
| | - Linao Ren
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, Hubei, PR China
| | - Zhaoxin Chen
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, Hubei, PR China
| | - Qi Wei
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, Hubei, PR China
| | - Song-Mei Liu
- Department of Clinical Laboratory, Center for Gene Diagnosis, and Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei, PR China
| | - Tian Feng
- School of Public Health, Wuhan University, Wuhan 430072, Hubei, PR China
| | - Bifeng Yuan
- School of Public Health, Wuhan University, Wuhan 430072, Hubei, PR China
| | - Xiaocheng Weng
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, Hubei, PR China
| | - Yuhao Du
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, Hubei, PR China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, Hubei, PR China
- Department of Hematology, Zhongnan Hospital, Wuhan University, Wuhan 430072, Hubei, PR China
- Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, Hubei, PR China
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4
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Varna D, Geromichalou E, Hatzidimitriou AG, Papi R, Psomas G, Dalezis P, Aslanidis P, Choli-Papadopoulou T, Trafalis DT, Angaridis PA. Silver(I) complexes bearing heterocyclic thioamide ligands with NH 2 and CF 3 substituents: effect of ligand group substitution on antibacterial and anticancer properties. Dalton Trans 2022; 51:9412-9431. [PMID: 35674362 DOI: 10.1039/d2dt00793b] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In recent years, there has been an increasing interest in the study of Ag(I) coordination compounds as potent antibacterial and anticancer agents. Herein, a series of Ag(I) complexes bearing phosphines and heterocyclic thioamide ligands with highly electronegative NH2- and CF3-group substituents, i.e. [AgCl(atdztH)(xantphos)] (1), [Ag(μ-atdztH)(DPEphos)]2(NO3)2 (2), [Ag(atdzt)(PPh3)3] (3), [Ag(μ-atdzt)(DPEphos)]2 (4), and [Ag(μ-mtft)(DPEphos)]2 (5), where atdztH = 5-amino-1,3,4-thiadiazole-2-thiol, mtftH = 4-methyl-5-(trifluoromethyl)-1,2,4-triazol-3-thiol, xantphos = 4,5-bis(diphenylphosphino)-9,9-dimethylxanthene, and DPEphos = bis(2-diphenylphosphino-phenyl)ether, were synthesized, and their in vitro antibacterial and anticancer properties were evaluated. Complexes 1-4 bearing the NH2-substituted thioamide exhibited moderate-to-high activity against S. aureus, B. subtilis, B. cereus and E. coli bacterial strains. A high antiproliferative activity was also observed for 1-3 against SKOV-3, Hup-T3, DMS114 and PC3 cancer cell lines (IC50 = 4.0-11.7 μM), as well as some degree of selectivity against MRC-5 normal cells. Interestingly, 5 bearing the CF3-substituted thioamide is completely inactive in all bioactivity studies. Binding of 1-3 to drug-carrier proteins BSA and HSA is reasonably strong for their uptake and subsequent release to possible target sites. The three complexes show a significant in vitro antioxidant ability for scavenging free radicals, suggesting likely implication of this property in the mechanism of their bioactivity, but a low potential to destroy the double-strand structure of CT-DNA by intercalation. Complementary insights into possible bioactivity mechanisms were provided by molecular docking calculations, exploring the ability of complexes to bind to bacterial DNA gyrase, and to the overexpressed in the aforementioned cancer cells Fibroblast Growth Factor Receptor 1, affecting their functionalities.
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Affiliation(s)
- Despoina Varna
- Laboratory of Inorganic Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Elena Geromichalou
- Laboratory of Pharmacology, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 11527 Athens, Greece.
| | - Antonios G Hatzidimitriou
- Laboratory of Inorganic Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Rigini Papi
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - George Psomas
- Laboratory of Inorganic Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Panagiotis Dalezis
- Laboratory of Pharmacology, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 11527 Athens, Greece.
| | - Paraskevas Aslanidis
- Laboratory of Inorganic Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Theodora Choli-Papadopoulou
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Dimitrios T Trafalis
- Laboratory of Pharmacology, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 11527 Athens, Greece.
| | - Panagiotis A Angaridis
- Laboratory of Inorganic Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
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5
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Mansha M, Taha M, Hassane Anouar E, Ullah N. The design of fluoroquinolone-based cholinesterase inhibitors: Synthesis, biological evaluation and in silico docking studies. ARAB J CHEM 2021. [DOI: 10.1016/j.arabjc.2021.103211] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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6
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Johnson BM, Shu YZ, Zhuo X, Meanwell NA. Metabolic and Pharmaceutical Aspects of Fluorinated Compounds. J Med Chem 2020; 63:6315-6386. [PMID: 32182061 DOI: 10.1021/acs.jmedchem.9b01877] [Citation(s) in RCA: 310] [Impact Index Per Article: 77.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The applications of fluorine in drug design continue to expand, facilitated by an improved understanding of its effects on physicochemical properties and the development of synthetic methodologies that are providing access to new fluorinated motifs. In turn, studies of fluorinated molecules are providing deeper insights into the effects of fluorine on metabolic pathways, distribution, and disposition. Despite the high strength of the C-F bond, the departure of fluoride from metabolic intermediates can be facile. This reactivity has been leveraged in the design of mechanism-based enzyme inhibitors and has influenced the metabolic fate of fluorinated compounds. In this Perspective, we summarize the literature associated with the metabolism of fluorinated molecules, focusing on examples where the presence of fluorine influences the metabolic profile. These studies have revealed potentially problematic outcomes with some fluorinated motifs and are enhancing our understanding of how fluorine should be deployed.
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Affiliation(s)
- Benjamin M Johnson
- Pharmaceutical Candidate Optimization, Bristol Myers Squibb Company, 100 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Yue-Zhong Shu
- Pharmaceutical Candidate Optimization, Bristol Myers Squibb Company, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Xiaoliang Zhuo
- Pharmaceutical Candidate Optimization, Bristol Myers Squibb Company, 100 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Nicholas A Meanwell
- Discovery Chemistry Platforms, Small Molecule Drug Discovery, Bristol Myers Squibb Company, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
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7
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Sudileti M, Nagaripati S, Gundluru M, Chintha V, Aita S, Wudayagiri R, Chamarthi N, Cirandur SR. rGO‐SO 3H Catalysed Green Synthesis of Fluoro‐Substituted Aminomethylene Bisphosphonates and their Anticancer, Molecular Docking studies. ChemistrySelect 2019. [DOI: 10.1002/slct.201903191] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Murali Sudileti
- Department of ChemistrySri Venkateswara University Tirupati 517 502, Andhra Pradesh India
| | | | - Mohan Gundluru
- Department of ChemistrySri Venkateswara University Tirupati 517 502, Andhra Pradesh India
- DST-PURSE CentreSri Venkateswara University Tirupati - 517 502, Andhra Pradesh India
| | - Venkataramaiah Chintha
- Department of ZoologySri Venkateswara University Tirupati - 517 502, Andhra Pradesh India
| | - Saikiran Aita
- Department of ChemistrySri Venkateswara University Tirupati 517 502, Andhra Pradesh India
| | - Rajendra Wudayagiri
- Department of ZoologySri Venkateswara University Tirupati - 517 502, Andhra Pradesh India
| | - Nagaraju Chamarthi
- Department of ChemistrySri Venkateswara University Tirupati 517 502, Andhra Pradesh India
| | - Suresh Reddy Cirandur
- Department of ChemistrySri Venkateswara University Tirupati 517 502, Andhra Pradesh India
- Institute of Food Security and Sustainable AgricultureUniversiti Malaysia Kelantan Kampus Jeli Locked Bag 100 17600 Jeli, Kelantan Malaysia
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8
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Mishra SK, Suryaprakash N. Intramolecular Hydrogen Bonding Involving Organic Fluorine: NMR Investigations Corroborated by DFT-Based Theoretical Calculations. Molecules 2017; 22:E423. [PMID: 28272370 PMCID: PMC6155419 DOI: 10.3390/molecules22030423] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 03/02/2017] [Indexed: 01/24/2023] Open
Abstract
The combined utility of many one and two dimensional NMR methodologies and DFT-based theoretical calculations have been exploited to detect the intramolecular hydrogen bond (HB) in number of different organic fluorine-containing derivatives of molecules, viz. benzanilides, hydrazides, imides, benzamides, and diphenyloxamides. The existence of two and three centered hydrogen bonds has been convincingly established in the investigated molecules. The NMR spectral parameters, viz., coupling mediated through hydrogen bond, one-bond NH scalar couplings, physical parameter dependent variation of chemical shifts of NH protons have paved the way for understanding the presence of hydrogen bond involving organic fluorine in all the investigated molecules. The experimental NMR findings are further corroborated by DFT-based theoretical calculations including NCI, QTAIM, MD simulations and NBO analysis. The monitoring of H/D exchange with NMR spectroscopy established the effect of intramolecular HB and the influence of electronegativity of various substituents on the chemical kinetics in the number of organic building blocks. The utility of DQ-SQ technique in determining the information about HB in various fluorine substituted molecules has been convincingly established.
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Affiliation(s)
- Sandeep Kumar Mishra
- NMR Research Centre, Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India.
| | - N Suryaprakash
- NMR Research Centre, Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India.
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9
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Lederer F, Vignaud C, North P, Bodevin S. Trifluorosubstrates as mechanistic probes for an FMN-dependent l-2-hydroxy acid-oxidizing enzyme. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1215-1221. [PMID: 27155230 DOI: 10.1016/j.bbapap.2016.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 04/17/2016] [Accepted: 05/03/2016] [Indexed: 11/29/2022]
Abstract
A controversy exists with respect to the mechanism of l-2-hydroxy acid oxidation by members of a family of FMN-dependent enzymes. A so-called carbanion mechanism was initially proposed, in which the active site histidine abstracts the substrate α-hydrogen as a proton, followed by electron transfer from the carbanion to the flavin. But an alternative mechanism was not incompatible with some results, a mechanism in which the active site histidine instead picks up the substrate hydroxyl proton and a hydride transfer occurs. Even though more recent experiments ruling out such a mechanism were published (Rao & Lederer (1999) Protein Science 7, 1531-1537), a few authors have subsequently interpreted their results with variant enzymes in terms of a hydride transfer. In the present work, we analyse the reactivity of trifluorolactate, a substrate analogue, with the flavocytochrome b2 (Fcb2) flavodehydrogenase domain, compared to its reactivity with an NAD-dependent lactate dehydrogenase (LDH), for which this compound is known to be an inhibitor (Pogolotti & Rupley (1973) Biochem. Biophys. Res. Commun, 55, 1214-1219). Indeed, electron attraction by the three fluorine atoms should make difficult the removal of the α-H as a hydride. We also analyse the reactivity of trifluoropyruvate with the FMN- and NAD-dependent enzymes. The results substantiate a different effect of the fluorine substituents on the two enzymes compared to their normal substrates. In the discussion we analyse the conclusions of recent papers advocating a hydride transfer mechanism for the family of l-2-hydroxy acid oxidizing FMN-dependent enzymes.
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Affiliation(s)
- Florence Lederer
- Laboratoire d'Enzymologie, UPR 9063, CNRS, 91198 Gif-sur-Yvette Cedex, France; Laboratoire de Chimie Physique, CNRS UMR 8000, Université Paris-Sud, Université Paris-Saclay, 91405 Orsay Cedex, France.
| | - Caroline Vignaud
- Laboratoire d'Enzymologie, UPR 9063, CNRS, 91198 Gif-sur-Yvette Cedex, France
| | - Paul North
- Laboratoire d'Enzymologie, UPR 9063, CNRS, 91198 Gif-sur-Yvette Cedex, France
| | - Sabrina Bodevin
- Laboratoire d'Enzymologie, UPR 9063, CNRS, 91198 Gif-sur-Yvette Cedex, France
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10
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Mishra SK, Suryaprakash N. Intramolecular hydrogen bonds involving organic fluorine in the derivatives of hydrazides: an NMR investigation substantiated by DFT based theoretical calculations. Phys Chem Chem Phys 2016; 17:15226-35. [PMID: 25993543 DOI: 10.1039/c5cp01505g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The rare examples of intramolecular hydrogen bonds (HB) of the type the N-H∙∙∙F-C, detected in a low polarity solvent in the derivatives of hydrazides, by utilizing one and two-dimensional solution state multinuclear NMR techniques, are reported. The observation of through-space couplings, such as, (1h)JFH, and (1h)JFN, provides direct evidence for the existence of intra-molecular HB. Solvent induced perturbations and the variable temperature NMR experiments unambiguously establish the presence of intramolecular HB. The existence of multiple conformers in some of the investigated molecules is also revealed by two dimensional HOESY and (15)N-(1)H HSQC experiments. The (1)H DOSY experimental results discard any possibility of self or cross dimerization of the molecules. The derived NMR experimental results are further substantiated by Density Function Theory (DFT) based Non Covalent Interaction (NCI), and Quantum Theory of Atom in Molecule (QTAIM) calculations. The NCI calculations served as a very sensitive tool for detection of non-covalent interactions and also confirm the presence of bifurcated HBs.
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Affiliation(s)
- Sandeep Kumar Mishra
- NMR Research Centre, Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore-560012, India.
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11
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Mishra SK, Suryaprakash N. Organic fluorine involved intramolecular hydrogen bonds in the derivatives of imides: NMR evidence corroborated by DFT based theoretical calculations. RSC Adv 2015. [DOI: 10.1039/c5ra19537c] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The rare occurrence of intramolecular hydrogen bonds (HBs) of the type N–H⋯F–C is detected in the derivatives of imides in a low polarity solvent by using multi-dimensional and multinuclear NMR experiments.
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Affiliation(s)
- Sandeep Kumar Mishra
- NMR Research Centre
- Solid State and Structural Chemistry Unit
- Indian Institute of Science
- Bangalore-560012
- India
| | - N. Suryaprakash
- NMR Research Centre
- Solid State and Structural Chemistry Unit
- Indian Institute of Science
- Bangalore-560012
- India
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12
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Bartolomé C, Villafañe F, Martín-Alvarez JM, Martínez-Ilarduya JM, Espinet P. [Pd(Fmes)2(tmeda)]: A Case of Intermittent CH⋅⋅⋅FC Hydrogen-Bond Interaction in Solution. Chemistry 2013; 19:3702-9. [DOI: 10.1002/chem.201203512] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Indexed: 11/08/2022]
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13
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Chaudhari SR, Mogurampelly S, Suryaprakash N. Engagement of CF3 Group in N–H···F–C Hydrogen Bond in the Solution State: NMR Spectroscopy and MD Simulation Studies. J Phys Chem B 2013; 117:1123-9. [DOI: 10.1021/jp310798d] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sachin Rama Chaudhari
- NMR
Research Centre, ‡Solid State and Structural Chemistry Unit, and §Department of Physics, Indian Institute of Science, Bangalore
560012, India
| | - Santosh Mogurampelly
- NMR
Research Centre, ‡Solid State and Structural Chemistry Unit, and §Department of Physics, Indian Institute of Science, Bangalore
560012, India
| | - N. Suryaprakash
- NMR
Research Centre, ‡Solid State and Structural Chemistry Unit, and §Department of Physics, Indian Institute of Science, Bangalore
560012, India
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14
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Sunil SL, Nayak SK, Hathwar VR, Chopra D, Guru Row TN. Role of Fluorine in Weak Interactions in Co-crystals. PHARMACEUTICAL SALTS AND CO-CRYSTALS 2011. [DOI: 10.1039/9781849733502-00029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The presence of the C–F bond (commonly referred to as organic fluorine) in a large number of pharmaceutically relevant compounds suggests that it may be used in the production of novel salts and co-crystals that have intermolecular interactions involving fluorine. There is an ongoing debate in this context as fluorine is characterized by its high electronegativity, relatively small size and very low polarizability. The propensity of hydrogen to participate in generating highly directional and energetically stable hydrogen bonds has been exploited in the design of co-crystals and salts of many pharmaceutical compounds. A direct extension of this property to fluorine, however, is not plausible and thus intermolecular interactions involving fluorine must be quantified. Recent results and new approaches designed to evaluate organic fluorine which provide useful inputs for the design of co-crystals and salts are discussed in this chapter.
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Affiliation(s)
- Seetha Lekshmi Sunil
- Solid State and Structural Chemistry Unit Indian Institute of Science, Bangalore 560012 India
| | - Susanta K. Nayak
- Solid State and Structural Chemistry Unit Indian Institute of Science, Bangalore 560012 India
| | - Venkatesha R. Hathwar
- Solid State and Structural Chemistry Unit Indian Institute of Science, Bangalore 560012 India
| | - Deepak Chopra
- Department of Chemistry Indian Institute of Science Education and Research, Bhopal, 462023 India
| | - Tayur N. Guru Row
- Solid State and Structural Chemistry Unit Indian Institute of Science, Bangalore 560012 India
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15
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16
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Caspase: The unfriendly “meat tenderizer” of sepsis*. Crit Care Med 2010; 38:2075-6. [DOI: 10.1097/ccm.0b013e3181f3dd8f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Kirsanova OV, Cherepanova NA, Gromova ES. Inhibition of C5-cytosine-DNA-methyltransferases. BIOCHEMISTRY (MOSCOW) 2009; 74:1175-86. [DOI: 10.1134/s0006297909110017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Sheflyan GY, Kubareva EA, Gromova ES. Methods for the covalent attachment of nucleic acids and their derivatives to proteins. RUSSIAN CHEMICAL REVIEWS 2007. [DOI: 10.1070/rc1996v065n08abeh000277] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Riley KE, Cui G, Merz KM. An ab Initio Investigation of the Interactions Involving the Aromatic Group of the Set of Fluorinated N-(4-Sulfamylbenzoyl)benzylamine Inhibitors and Human Carbonic Anhydrase II. J Phys Chem B 2007; 111:5700-7. [PMID: 17474767 DOI: 10.1021/jp067313m] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work we investigate the interactions that occur between the aromatic portion of the set of fluorinated N-(4-sulfamylbenzoyl)benzylamine (SBB) inhibitors and two residues of Human Carbonic Anhydrase II (HCAII), namely Phe-131 and Pro-202. Calculations were carried out at the MP2/aug-cc-pVDZ level of theory and the counterpoise scheme of Boys and Bernardi was employed to account for the basis set superposition error. The most striking result obtained here is that the SBB phenyl ring interacts at least as strongly with the proline pyrrolidine ring as with the phenylalanine phenyl ring, which is surprising because aromatic-aromatic interactions have long been thought to be particularly favorable in protein and protein-ligand structure. Comparison of the MP2 binding energies to those obtained with the Hartree-Fock method indicates that the attraction between the proline pyrrolidine ring and the SBB phenyl ring is largely attributable to dispersion forces. These favorable interactions between pyrrolidine and phenyl rings may have important implications in protein structure because there is potential for proline residues to interact with phenylalanine residues in a fashion analogous to that seen here. A preliminary protein data bank search indicates that the proline-phenylalanine contacts are about 40% as common as those between two phenylalanines. It is also found here that the number and pattern of fluorine substituents on the SBB phenyl ring is much less important in determining the SBB-HCAII binding energy than the relative geometric configuration of the interacting pairs.
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Affiliation(s)
- Kevin E Riley
- Quantum Theory Project and Department of Chemistry, The University of Florida, Gainesville, Florida 32611-8435, USA
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21
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Li G, van der Donk WA. Efficient synthesis of suitably protected beta-difluoroalanine and gamma-difluorothreonine from L-ascorbic acid. Org Lett 2007; 9:41-4. [PMID: 17192080 PMCID: PMC2593874 DOI: 10.1021/ol062401a] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] Fluorinated amino acids are useful building blocks for the preparation of biologically active peptides and peptidomimetics with increased metabolic stability. We report here the synthesis of two fluorinated amino acids, beta-difluoroalanine and gamma-difluorothreonine, as analogues of Ser and Thr, respectively. These compounds were suitably protected for Fmoc-based solid-phase peptide synthesis. Once incorporated into peptides, they may serve as alternative substrates or inhibitors of lantibiotic synthetases that posttranslationally dehydrate Ser and Thr residues to dehydroalanine and dehydrobutyrine, respectively.
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Bartolomé C, Espinet P, Martín-Alvarez JM. Is there any bona fide example of O–H⋯F–C bond in solution? The cases of HOC(CF3)2(4-X-2,6-C6H2(CF3)2) (X = Si(i-Pr)3, CF3). Chem Commun (Camb) 2007:4384-6. [DOI: 10.1039/b710304b] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Canova S, Bellosta V, Mignani S, Bigot A, Cossy J. Rearrangement of Homoallylic Alcohols Induced by DAST. Org Lett 2006; 8:2091-4. [PMID: 16671789 DOI: 10.1021/ol060529m] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[reaction: see text] Treatment of beta,gamma-unsaturated monoprotected 1,2-diols with diethylaminosulfur trifluoride (DAST) allows the stereoselective formation of beta,gamma-unsaturated aldehydes in good yields and with a good transfer of chirality.
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Affiliation(s)
- Sophie Canova
- Laboratoire de Chimie Organique, Associé au CNRS, Paris, France
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Riley KE, Merz KM. Effects of Fluorine Substitution on the Edge-to-Face Interaction of the Benzene Dimer. J Phys Chem B 2005; 109:17752-6. [PMID: 16853270 DOI: 10.1021/jp052411d] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To gain some insight into the effects of fluorination on the aromatic-aromatic interactions found in protein-ligand complexes, like those observed in the set of N-(4-sulfamylbenzoyl)benzylamine (SBB) inhibitors bound to Human Carbonic Anhydrase II (HCAII), we have produced potential energy curves for the edge-to-face interactions of a set of fluorinated benzene dimer compounds. All calculations were carried out at the MP2/aug-cc-pVDZ level of theory using the counterpoise method of Boys and Bernardi (Boys, S. F.; Bernardi, F. Mol. Phys. 1970, 19, 553) to account for the basis set superposition error. Fluorine substitutions are made onto the face molecule of the edge-to-face benzene dimer. As one might expect, the substitution of additional fluorines into this system generally resulted in a decrease of the binding energy. It was also found that the positioning of the fluorine substituents on isosubstituted compounds has a large effect on the total binding energy of these types of systems. More specifically, complexes with fluorines that are substituted closer to the hydrogen atoms of the edge benzene will tend to be stabilized by an electrostatic interaction between the partially negative fluorine atoms and the partially positive hydrogen atoms. However, our findings do not explain the recent crystallographic findings for the SBB-HCAII protein-ligand complex, where increased fluorination resulted in closer edge-to-face contacts, which suggests that there are factors, other than edge-to-face aromatic interactions, influencing this system's behavior.
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Affiliation(s)
- Kevin E Riley
- 104 Chemistry Building, Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Zhou H, Schmidt DMZ, Gerlt JA, van der Donk WA. Chemical and enzymatic synthesis of fluorinated-dehydroalanine-containing peptides. Chembiochem 2004; 4:1206-15. [PMID: 14613113 DOI: 10.1002/cbic.200300654] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Michael acceptors have long been recognized as reactive functionalities that may link a biologically active molecule to its cellular target. 1,2-Dehydro amino acids are potential Michael acceptors present in a large number of natural products, but their reactivity is modulated by the deactivating nature of the alpha-amino group engaged in an amide bond. We describe here the preparation of 3-fluoro-1,2-dehydroalanine moieties within peptides that significantly enhance the reactivity of the Michael acceptor. Two different routes were designed to access these compounds, one relying on chemical means to introduce the desired functionality and the second taking advantage of a peptide epimerase. In the chemical approach, the fluoro-Pummerer reaction of cysteine derivatives afforded 3-fluorocysteine residues that were oxidized to the corresponding sulfoxides, followed by thermolytic elimination to provide the desired 3-fluorodehydroalanines. The mechanism of the fluoro-Pummerer reaction was investigated and several possible pathways were ruled out. The enzymatic approach utilized the dipeptide epimerase YcjG from Escherichia coli. Difluorinated alanine was incorporated at the C terminus of a dipeptide by chemical means. The resulting peptide proved to be a substrate for YcjG, which catalyzed fluoride elimination to provide the 3-fluorodehydroalanine-containing peptide. Mechanistic investigations showed that fluoride elimination occurred faster than epimerization and at a rate close to that of epimerization of Ala-Ala.
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Affiliation(s)
- Hao Zhou
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
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Kasuya MCZ, Cusi R, Ishihara O, Miyagawa A, Hashimoto K, Sato T, Hatanaka K. Fluorous-tagged compound: a viable scaffold to prime oligosaccharide synthesis by cellular enzymes. Biochem Biophys Res Commun 2004; 316:599-604. [PMID: 15033442 DOI: 10.1016/j.bbrc.2004.02.094] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2004] [Indexed: 11/23/2022]
Abstract
Fluorous-tagged saccharide primers could be viable scaffolds for the synthesis of oligosaccharides. This research demonstrates that a fluorine-containing saccharide derivative could actually be taken up by the cell, the saccharide chain elongated by cellular enzymes, and the elongated product released by the cells to the culture medium. A fluorous-tagged lactoside primer, 6-(perfluorohexyl)hexyl-4-O-(beta-D-galactopyranosyl)-beta-D-glucopyranoside, was chemically synthesized and introduced in mouse B16 cells to prime oligosaccharide synthesis. Uptake of the primer by B16 cells resulted in the sialylation of the terminal galactose residue to afford an oligosaccharide with the same glycan structure as ganglioside GM3. The presence of many fluorine atoms did not have any adverse effects to the cells. Moreover, the number of fluorine atoms did not pose a steric barrier and instead, their presence possibly increased the hydrophobicity of the primer and enhanced membrane permeability. This strategy of using a fluorous-tagged primer and cells can pave the way for an easier way of preparing oligosaccharides via an environment-friendly approach that eliminates the use of large amounts of organic solvents.
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Affiliation(s)
- Maria Carmelita Z Kasuya
- Institute of Industrial Science, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
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Wölker D, Haufe G. Synthesis of optically active vicinal fluorohydrins by lipase-catalyzed deracemization. J Org Chem 2002; 67:3015-21. [PMID: 11975561 DOI: 10.1021/jo016331r] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Three microbial lipases have been used to deracemize trans-2-fluorocycloalkanols 2 both by hydrolysis of the corresponding acetates 3 or chloroacetates 4 and by esterification of the fluorohydrins 2 using vinyl acetate and vinyl chloroacetate, respectively. Pseudomonas cepacia lipase was the most selective for the six- and the seven-membered-ring compounds, while the lipase from Candida rugosa was most useful for the eight-membered-ring compounds. Both lipases transform the (R)-enantiomers preferentially. In contrast the lipase from Candida antarctica hydrolyzed the esters of trans-2-fluorocyclohexanol 2a and esterified the fluorohydrin itself with very low enantiopreference for the (R)-isomers. The seven- and the eight-membered ring esters and the corresponding fluorohydrins were also transformed with low, but reverse, enantioselectivity.
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Affiliation(s)
- Dörthe Wölker
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstr. 40, D-48149 Münster, Germany
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Haufe G, Rosen TC, Meyer OG, Fröhlich R, Rissanen K. Synthesis, reactions and structural features of monofluorinated cyclopropanecarboxylates. J Fluor Chem 2002. [DOI: 10.1016/s0022-1139(02)00040-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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30
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Barbarich TJ, Nolan BG, Tsujioka S, Miller SM, Anderson OP, Strauss SH. New or improved syntheses of the polyfluoroalcohols HOC(cyclo-C6H11)2(CF3), HO(cyclo-C6H11)(CF3)2, and HOC(Ar)(CF3)2 (Ar = 4-C6H4(t-Bu), 2,4,6-C6H2(CF3)3, 4-Si(i-Pr)3-2,6-C6H2(CF3)2, 3,5-C6H3(CH3)2), and 2-C6H4(C(OH)(CF3)2). J Fluor Chem 2001. [DOI: 10.1016/s0022-1139(01)00471-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Abstract
[reaction: see text] Peptides containing (E)- and (Z)-3-fluorodehydroalanine have been prepared from serine via a fluoro-Pummerer rearrangement. The resulting electrophilic moieties may be useful affinity labels for the identification of the targets of dehydroamino acid containing natural products that act by covalent mechanisms.
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Affiliation(s)
- H Zhou
- Department of Chemistry, University of Illinois at Urbana-Champaign, 61801, USA
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Kim CY, Chang JS, Doyon JB, Baird, TT, Fierke CA, Jain A, Christianson DW. Contribution of Fluorine to Protein−Ligand Affinity in the Binding of Fluoroaromatic Inhibitors to Carbonic Anhydrase II. J Am Chem Soc 2000. [DOI: 10.1021/ja002627n] [Citation(s) in RCA: 109] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Chu-Young Kim
- Contribution from Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, Department of Chemistry, Swarthmore College, Swarthmore, Pennsylvania 19081-1397, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94143, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, and Department of Chemistry, University of California, Berkeley, Berkeley, California 94720
| | - Jeanne S. Chang
- Contribution from Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, Department of Chemistry, Swarthmore College, Swarthmore, Pennsylvania 19081-1397, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94143, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, and Department of Chemistry, University of California, Berkeley, Berkeley, California 94720
| | - Jeffrey B. Doyon
- Contribution from Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, Department of Chemistry, Swarthmore College, Swarthmore, Pennsylvania 19081-1397, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94143, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, and Department of Chemistry, University of California, Berkeley, Berkeley, California 94720
| | - Teaster T. Baird,
- Contribution from Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, Department of Chemistry, Swarthmore College, Swarthmore, Pennsylvania 19081-1397, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94143, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, and Department of Chemistry, University of California, Berkeley, Berkeley, California 94720
| | - Carol A. Fierke
- Contribution from Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, Department of Chemistry, Swarthmore College, Swarthmore, Pennsylvania 19081-1397, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94143, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, and Department of Chemistry, University of California, Berkeley, Berkeley, California 94720
| | - Ahamindra Jain
- Contribution from Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, Department of Chemistry, Swarthmore College, Swarthmore, Pennsylvania 19081-1397, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94143, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, and Department of Chemistry, University of California, Berkeley, Berkeley, California 94720
| | - David W. Christianson
- Contribution from Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, Department of Chemistry, Swarthmore College, Swarthmore, Pennsylvania 19081-1397, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94143, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, and Department of Chemistry, University of California, Berkeley, Berkeley, California 94720
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Grée D, Madiot V, Grée R. High regio-and stereocontrol in the dehydroxy — fluorination of propargylic alcohols and the corresponding Cobalt-carbonyl complexes. Tetrahedron Lett 1999. [DOI: 10.1016/s0040-4039(99)01329-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Legoupy S, Crévisy C, Guillemin JC, Grée R. Regio- and stereoselective allylic fluorination using chiral rhenium complexes. J Fluor Chem 1999. [DOI: 10.1016/s0022-1139(98)00305-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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38
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Kaul PN. Drug discovery: past, present and future. PROGRESS IN DRUG RESEARCH. FORTSCHRITTE DER ARZNEIMITTELFORSCHUNG. PROGRES DES RECHERCHES PHARMACEUTIQUES 1998; 50:9-105. [PMID: 9670776 DOI: 10.1007/978-3-0348-8833-2_1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
New drug discovery from early on involved a trial-and-error approach on naturally derived materials and substances until the end of the nineteenth century. The first half of the twentieth century witnessed systematic pharmacological evaluations of both natural and synthetic compounds. However, most new drugs until the 1970s were discovered by serendipity. With the exponential development of molecular biology on one hand and computer technology on the other, it became possible from 1980 onwards to place drug discovery on a rational basis. Cloning of genes has led to the development of methodologies for specific receptor-directed and enzyme-directed drug discoveries. Advances in recombinant DNA and transgenic technologies have enabled the production of human hormonal and other endogenous biomolecules as new drugs. As we understand more about the co-ordinating and regulating powers of the cerebral cortex during the next century, especially of the frontal lobe, man may be able to use bio-feedback training to voluntarily regulate the release of neurotransmitters, hormones, and other molecules involved in the regulation of various physiological processes in health as well as in disease.
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Affiliation(s)
- P N Kaul
- Clark Atlanta University, GA 30314, USA
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39
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Boukerb A, Grée D, Laabassi M, Grée R. Substituent effects on the regioselectivity in fluorination of allylic alcohols with DAST. J Fluor Chem 1998. [DOI: 10.1016/s0022-1139(98)00115-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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40
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Trifluoromethylketones chemistry: efficient access to silyl enol ethers or silyl carbinols using lithium diisopropylamide. J Fluor Chem 1997. [DOI: 10.1016/s0022-1139(97)00098-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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41
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Dancer JE, Ford MJ, Hamilton K, Kilkelly M, Lindell SD, O'Mahony MJ, Saville-Stones EA. Synthesis of potent inhibitors of histidinol dehydrogenase. Bioorg Med Chem Lett 1996. [DOI: 10.1016/0960-894x(96)00384-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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42
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Kermarrec C, Madiot V, Grée D, Meyer A, Grée R. A new highly stereoselective monofluorination in benzylic position. Tetrahedron Lett 1996. [DOI: 10.1016/0040-4039(96)01194-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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43
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Schirlin D, Baltzer S, Altenburger J, Tarnus C, Remy J. Difluoromethyleneketone retroamide, a versatile concept of inactivation of proteolytic enzymes. Tetrahedron 1996. [DOI: 10.1016/0040-4020(95)00896-g] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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44
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Neises B, Broersma RJ, Tarnus C, Piriou F, Remy JM, Lintz C, Heminger EF, Kutcher LW. Synthesis and comparison of tripeptidylfluoroalkane thrombin inhibitors. Bioorg Med Chem 1995; 3:1049-61. [PMID: 7582979 DOI: 10.1016/0968-0896(95)00097-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Fluorinated ketone thrombin inhibitors based on the peptide sequence methyl-(D)-Phe-Pro-Arg-CF2R were synthesized: MDL 73,446 (1, R = F); MDL 73,775 (2, R = CF3); and MDL 75,579 (3, R = CH2CH2CH3). These were shown to be highly effective, slow binding inhibitors of thrombin. Anticoagulant activity was dose-dependent with 3 > 2 > 1 at doubling thrombin time and APTT, respectively. Anticoagulant activity corresponded with efficacy in a platelet-dependent (FeCl3-induced) rat carotid artery thrombosis model. Arterial occlusion was dose-dependently prolonged with 3 > 2 > 1 at doubling the occlusion time.
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Affiliation(s)
- B Neises
- Marion Merrell Dow Research Institute, Strasbourg, France
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Fluoro-β-lactams: Synthesis and application in asymmetric synthesis. ACTA ACUST UNITED AC 1995. [DOI: 10.1016/s1572-5995(06)80066-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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47
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Antonino LC, Wu JC. Human IMP dehydrogenase catalyzes the dehalogenation of 2-fluoro- and 2-chloroinosine 5'-monophosphate in the absence of NAD. Biochemistry 1994; 33:1753-9. [PMID: 7906542 DOI: 10.1021/bi00173a018] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The ability of human type II inosine monophosphate dehydrogenase (IMPDH, EC 1.1.1.205) to catalyze the formation of xanthosine 5'-monophosphate (XMP) from C2 halogen-substituted analogs of IMP has been investigated. Adenosine deaminase was used to enzymatically synthesize 2-fluoroinosine and 2-chloroinosine from the 2-fluoro- and 2-chloroadenosine nucleoside analogs. Chemical phosphorylation yielded the corresponding 5'-nucleoside monophosphate derivatives. IMPDH catalyzes the conversion of both 2-fluoro- and 2-chloroinosine 5'-monophosphate (2-F- and 2-Cl-IMP) to XMP. The dehalogenation reactions proceed without nicotinamide adenine dinucleotide (NAD), the hydride acceptor required for the oxidation of IMP, the normal substrate of the enzyme. Formation of XMP from the 2-halo-IMPs was verified by UV absorption spectroscopy and by HPLC. Formation of XMP from 2-F-IMP yielded stoichiometric amounts of fluoride anion. IMP and XMP were competitive inhibitors toward 2-Cl-IMP in the dehalogenation reaction. Neither 2-F-IMP nor 2-Cl-IMP irreversibly inactivate IMPDH. Kinetic constants for the dehalogenation reactions have been determined and compared to the dehydrogenation reaction at 25 degrees C. (For 2-F-IMP: kcat = 0.058 s-1, Km = 62 microM. For 2-Cl-IMP: kcat = 0.049 s-1, Km = 48 microM. For the IMP dehydrogenation reaction: kcat = 0.25 s-1, Km [IMP] = 4.1 microM, Km [NAD] = 29 microM). Hydrolytic dehalogenation of 2-halo-IMPs without a requirement for NAD demonstrates the formation of a tetrahedral intermediate in the catalytic mechanism of IMP dehydrogenase.
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Affiliation(s)
- L C Antonino
- Institute of Biochemistry and Cell Biology, Syntex Discovery Research, Palo Alto, California 94304
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48
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Neder KM, French SA, Miller SP. Synthesis and inhibitory activity of difluoroketone substrate analogs of N-myristoyltransferase. Tetrahedron 1994. [DOI: 10.1016/s0040-4020(01)89601-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Abstract
The isoprenylation pathway requires an endoprotease that cleaves the modified protein at the isoprenylated cysteine residue. This endoprotease was readily assayed with simple tetrapeptide substrates of the type N-acetyl-S-farnesyl-L-Cys-(AFC)-Val-Ile-Met, where AFC and the tripeptide are the products of the hydrolysis. The endoprotease proved to be unaffected by (1) serine protease inhibitors, including (4-amidinophenyl)methanesulfonyl fluoride, aprotinin, and leupeptin, by (2) cysteine protease inhibitors, including E-64 and leupeptin [the enzyme is, however, inhibited by p-(hydroxymercuri)benzoate], by (3) metalloprotease inhibitors, including phosphoramidon, EDTA, and 1,10-phenanthroline, or by (4) the aspartyl protease inhibitor pepstatin. The conclusion from these data is that the enzyme is probably not a metalloenzyme. N-Boc-S-all-trans-farnesyl-L-cysteine (BFC) derivatives containing a statine moiety are also not inhibitory, strongly suggesting that the enzyme is not an aspartyl protease. However, the enzyme is potently inhibited by the aldehyde derivative of BFC (K1 = 1.9 microM), which is consistent with the idea that the enzyme is a serine or cysteine protease. Potent tetrapeptide-based competitive inhibitors were prepared. Analogs with the scissile bond modified so that hydrolysis could not occur were excellent inhibitors. An analog containing BFC-statine-Val-Ile-Met inhibited the endoprotease with a K1 = 64 nM. The equivalent pseudopeptide psi (CH2-NH) analog was almost as potent, indicating that the statine moiety simply represents a nonhydrolyzable linker.
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Affiliation(s)
- Y T Ma
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
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Neises B, Tarnus C, Broersma RJ, Bald C, Rémy JM, Heminger EF. The synthesis and anticoagulant activity of novel peptidylfluoroalkanes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1993; 340:185-8. [PMID: 8154335 DOI: 10.1007/978-1-4899-2418-6_16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- B Neises
- Marion-Merrell-Dow Research Institute, Strasbourg, France
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